That was the fate of the first-known church built for the parish, and the remains of the foundations are believed to be under the cathedral's Nave. For some time, the dispossessed parishioners heard Mass in the western end of the original Norman cathedral, their children were baptised in the cathedral font and the dead buried in the cathedral graveyard.

When the Nave of the cathedral was enlarged between 1192 and 1235, the chapel of Magdalene was set aside for the parishioners. It was removed and placed outside in the churchyard for the convenience of the parishioners, and then became known as the church of St Mary Magdalene. But when the cathedral Close wall was built, the parishioners yet again found themselves unable to gain access and once more were dispossessed.

As a consequence, in the late 13th century, Bishop Sutton(1280─1299) had a new church built beside the Exchequergate, where the present church building stands. The medieval church was largely destroyed during the English Civil War (1642─1649), and was rebuilt during the late-17th century. A further restoration took place in the Victorian period in 1882.

The church still contains fragments of the original medieval building, including one of Lincolnshire's oldest bells, dating back to 1350. This bell is still rung before services calling people to prayer as it did over six hundred years ago. The vicarage on the north side of the church was pulled down and became built on as extension of the White Hart Hotel. The parish registers include the baptisms and burials of many of the prisoners in Lincoln Castle.